Contacts of the helix formed by residues 115 - 131 (chain B) in PDB entry 5LXX
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 115 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110B PRO* 3.9 1.3 - - - +
114B THR* 1.3 78.1 + - - +
116B LEU* 1.3 63.8 + - - +
117B LEU* 3.7 5.3 + - - +
118B ALA* 3.0 32.0 + - - +
119B ALA* 3.3 19.6 + - - +
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Residues in contact with LEU 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B VAL* 4.4 2.9 - - - +
110B PRO* 3.6 27.1 - - + -
114B THR 3.8 2.4 + - - +
115B SER* 1.3 73.7 - - - +
117B LEU* 1.3 58.0 + - - +
119B ALA* 3.3 3.1 + - - +
120B PHE* 2.9 29.1 + - - +
139B VAL* 4.2 21.6 - - + +
140B ASP 4.1 9.6 - - - +
141B ILE* 4.5 24.9 - - + -
142B SER* 5.2 1.1 - - - +
143B GLU 6.0 0.4 - - - +
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Residues in contact with LEU 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B SER* 3.3 5.8 + - - +
116B LEU* 1.3 77.2 - - - +
118B ALA* 1.3 66.1 + - - +
120B PHE* 3.2 15.2 + - + -
121B ASP* 2.8 47.9 + - - +
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Residues in contact with ALA 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B THR* 5.9 2.2 - - - -
115B SER* 3.0 26.5 + - - +
117B LEU* 1.3 77.3 - - - +
119B ALA* 1.3 62.2 + - - +
121B ASP* 3.4 8.6 + - - +
122B GLN* 3.1 22.0 + - - +
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Residues in contact with ALA 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B VAL* 3.5 19.5 - - + -
110B PRO* 3.7 35.2 - - + -
114B THR* 5.4 0.4 - - - +
115B SER 3.3 3.7 + - - +
116B LEU 3.7 3.8 - - - +
117B LEU 3.2 0.2 - - - -
118B ALA* 1.3 77.7 - - - +
120B PHE* 1.3 64.4 + - - +
122B GLN* 3.1 6.5 + - - +
123B TRP* 2.9 37.0 + - + +
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Residues in contact with PHE 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B VAL* 3.5 12.0 - - + +
116B LEU 2.9 17.4 + - - +
117B LEU* 3.6 17.9 - - + +
119B ALA* 1.3 77.0 - - - +
121B ASP* 1.3 68.1 + - - +
123B TRP* 3.3 1.9 + - - +
124B ARG* 2.9 68.9 + - + +
137B LEU* 3.8 28.7 - - + -
139B VAL* 4.1 23.8 - - + -
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Residues in contact with ASP 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B LEU* 2.8 42.5 + - - +
118B ALA* 3.6 7.6 - - - +
120B PHE* 1.3 82.6 - - - +
122B GLN* 1.3 58.5 + - - +
124B ARG* 3.4 6.8 + - - +
125B GLU* 2.9 28.4 + - - +
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Residues in contact with GLN 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118B ALA 3.1 13.1 + - - +
119B ALA* 3.1 12.0 + - - +
121B ASP* 1.3 74.3 - - - +
123B TRP* 1.3 69.9 + - + +
125B GLU* 3.2 23.1 + - - +
126B TRP* 3.0 63.6 + - + +
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Residues in contact with TRP 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B PHE 4.4 4.0 + - - -
78B MET* 4.6 6.0 - - + +
79B PRO* 3.8 33.4 - - + -
89B PHE* 3.9 27.7 - + - -
106B ASP* 3.7 10.1 + - - -
107B HIS 3.1 24.1 + - - -
108B VAL* 3.8 21.8 - - + -
109B VAL* 3.5 44.0 - - + -
119B ALA* 2.9 39.0 + - + +
120B PHE 3.8 3.4 - - - +
122B GLN* 1.3 81.2 - - + +
124B ARG* 1.3 58.6 + - - +
126B TRP* 3.3 29.4 + + - +
127B ALA* 2.9 32.0 + - - +
137B LEU* 4.2 12.1 - - + -
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Residues in contact with ARG 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120B PHE* 2.9 53.7 + - + +
121B ASP* 3.6 7.4 - - - +
123B TRP* 1.3 74.1 - - - +
125B GLU* 1.3 60.4 + - - +
128B ASP* 2.7 64.4 + - - +
135B TYR* 3.1 25.3 + - - -
137B LEU* 3.8 15.9 - - + -
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Residues in contact with GLU 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B ASP 2.9 14.8 + - - +
122B GLN* 3.2 28.5 + - - +
124B ARG* 1.3 75.9 - - - +
126B TRP* 1.3 68.7 + - + +
128B ASP* 4.1 3.7 - - - +
129B SER* 3.1 27.2 + - - +
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Residues in contact with TRP 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B GLN* 3.4 50.2 - - + +
79B PRO* 4.2 20.4 - - + -
89B PHE* 3.9 15.2 - + + +
122B GLN* 3.0 47.7 + - + +
123B TRP* 3.6 53.8 - + - +
125B GLU* 1.3 83.3 + - + +
127B ALA* 1.3 61.3 - - - +
129B SER* 2.9 19.9 + - - -
130B LYS* 3.1 17.0 + - - +
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Residues in contact with ALA 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89B PHE* 3.8 33.9 - - + -
123B TRP 2.9 18.9 + - - +
126B TRP* 1.3 71.6 - - - +
128B ASP* 1.3 62.6 + - - +
131B SER* 2.8 32.9 + - - +
135B TYR* 3.3 36.2 - - + -
137B LEU* 5.5 0.2 - - + -
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Residues in contact with ASP 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B ARG* 2.7 58.4 + - - +
125B GLU* 4.1 4.2 - - - +
127B ALA* 1.3 73.7 - - - +
129B SER* 1.3 61.6 + - - +
131B SER 4.8 2.4 + - - +
135B TYR* 2.6 28.8 + - - -
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Residues in contact with SER 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B GLU* 3.1 15.9 + - - +
126B TRP* 2.9 18.0 + - - -
128B ASP* 1.3 78.2 - - - +
130B LYS* 1.3 73.6 + - - +
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Residues in contact with LYS 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B GLN* 3.7 28.8 - - - +
88B ASP* 3.4 28.5 - - - +
89B PHE* 3.8 2.7 - - + -
90B PHE* 3.4 41.7 - - + +
126B TRP* 3.1 11.1 + - - +
129B SER* 1.3 92.3 + - - +
131B SER* 1.3 68.4 + - - +
132B CYS* 3.3 1.9 + - - -
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Residues in contact with SER 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B PHE* 3.7 7.5 - - - +
93B THR* 3.4 21.1 - - - +
127B ALA* 2.8 31.9 + - - +
128B ASP 4.7 1.8 - - - +
129B SER 4.0 0.2 - - - -
130B LYS* 1.3 73.9 - - - +
132B CYS* 1.3 61.5 + - - +
133B CYS* 2.7 29.3 + - - +
135B TYR* 4.2 14.4 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il